Genotype- and tissue-specific miRNA profiles and their targets in three alfalfa (Medicago sativa L) genotypes
Abstract Background Alfalfa (Medicago sativa L.) is a forage legume with significant agricultural value worldwide. MicroRNAs (miRNAs) are key components of post-transcriptional gene regulation and essentially regulate many aspects of plant growth and development. Although miRNAs were reported in alf...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2018-12-01
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| Series: | BMC Genomics |
| Online Access: | http://link.springer.com/article/10.1186/s12864-018-5280-y |
| _version_ | 1819060540849258496 |
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| author | Robert Pokoo Shuchao Ren Qingyi Wang Christy M. Motes Timothy D. Hernandez Sayvan Ahmadi Maria J. Monteros Yun Zheng Ramanjulu Sunkar |
| author_facet | Robert Pokoo Shuchao Ren Qingyi Wang Christy M. Motes Timothy D. Hernandez Sayvan Ahmadi Maria J. Monteros Yun Zheng Ramanjulu Sunkar |
| author_sort | Robert Pokoo |
| collection | DOAJ |
| description | Abstract Background Alfalfa (Medicago sativa L.) is a forage legume with significant agricultural value worldwide. MicroRNAs (miRNAs) are key components of post-transcriptional gene regulation and essentially regulate many aspects of plant growth and development. Although miRNAs were reported in alfalfa, their expression profiles in different tissues and the discovery of novel miRNAs as well as their targets have not been described in this plant species. Results To identify tissue-specific miRNA profiles in whole plants, shoots and roots of three different alfalfa genotypes (Altet-4, NECS-141and NF08ALF06) were used. Small RNA libraries were generated and sequenced using a high-throughput sequencing platform. Analysis of these libraries enabled identification of100 miRNA families; 21 of them belong to the highly conserved families while the remaining 79 families are conserved at the minimum between M. sativa and the model legume and close relative, M. truncatula. The profiles of the six abundantly expressed miRNA families (miR156, miR159, miR166, miR319, miR396 and miR398) were relatively similar between the whole plants, roots and shoots of these three alfalfa genotypes. In contrast, robust differences between shoots and roots for miR160 and miR408 levels were evident, and their expression was more abundant in the shoots. Additionally, 17 novel miRNAs were identified and the relative abundance of some of these differed between tissue types. Further, the generation and analysis of degradome libraries from the three alfalfa genotypes enabled confirmation of 69 genes as targets for 31 miRNA families in alfalfa. Conclusions The miRNA profiles revealed both similarities and differences in the expression profiles between tissues within a genotype as well as between the genotypes. Among the highly conserved miRNA families, miR166 was the most abundantly expressed in almost all tissues from the three genotypes. The identification of conserved and novel miRNAs as well as their targets in different tissues of multiple genotypes increased our understanding of miRNA-mediated gene regulation in alfalfa and could provide valuable insights for practical research and plant improvement applications in alfalfa and related legume species. |
| first_indexed | 2024-12-21T14:28:37Z |
| format | Article |
| id | doaj.art-2bd4d296b0124c61aba54e6573710091 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-21T14:28:37Z |
| publishDate | 2018-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-2bd4d296b0124c61aba54e65737100912022-12-21T19:00:34ZengBMCBMC Genomics1471-21642018-12-0119S1011513110.1186/s12864-018-5280-yGenotype- and tissue-specific miRNA profiles and their targets in three alfalfa (Medicago sativa L) genotypesRobert Pokoo0Shuchao Ren1Qingyi Wang2Christy M. Motes3Timothy D. Hernandez4Sayvan Ahmadi5Maria J. Monteros6Yun Zheng7Ramanjulu Sunkar8Department of Biochemistry and Molecular Biology, Oklahoma State UniversityInstitute of Primate Translational Medicine, Kunming University of Science and TechnologyInstitute of Primate Translational Medicine, Kunming University of Science and TechnologyNoble Research InstituteNoble Research InstituteDepartment of Biochemistry and Molecular Biology, Oklahoma State UniversityNoble Research InstituteInstitute of Primate Translational Medicine, Kunming University of Science and TechnologyDepartment of Biochemistry and Molecular Biology, Oklahoma State UniversityAbstract Background Alfalfa (Medicago sativa L.) is a forage legume with significant agricultural value worldwide. MicroRNAs (miRNAs) are key components of post-transcriptional gene regulation and essentially regulate many aspects of plant growth and development. Although miRNAs were reported in alfalfa, their expression profiles in different tissues and the discovery of novel miRNAs as well as their targets have not been described in this plant species. Results To identify tissue-specific miRNA profiles in whole plants, shoots and roots of three different alfalfa genotypes (Altet-4, NECS-141and NF08ALF06) were used. Small RNA libraries were generated and sequenced using a high-throughput sequencing platform. Analysis of these libraries enabled identification of100 miRNA families; 21 of them belong to the highly conserved families while the remaining 79 families are conserved at the minimum between M. sativa and the model legume and close relative, M. truncatula. The profiles of the six abundantly expressed miRNA families (miR156, miR159, miR166, miR319, miR396 and miR398) were relatively similar between the whole plants, roots and shoots of these three alfalfa genotypes. In contrast, robust differences between shoots and roots for miR160 and miR408 levels were evident, and their expression was more abundant in the shoots. Additionally, 17 novel miRNAs were identified and the relative abundance of some of these differed between tissue types. Further, the generation and analysis of degradome libraries from the three alfalfa genotypes enabled confirmation of 69 genes as targets for 31 miRNA families in alfalfa. Conclusions The miRNA profiles revealed both similarities and differences in the expression profiles between tissues within a genotype as well as between the genotypes. Among the highly conserved miRNA families, miR166 was the most abundantly expressed in almost all tissues from the three genotypes. The identification of conserved and novel miRNAs as well as their targets in different tissues of multiple genotypes increased our understanding of miRNA-mediated gene regulation in alfalfa and could provide valuable insights for practical research and plant improvement applications in alfalfa and related legume species.http://link.springer.com/article/10.1186/s12864-018-5280-y |
| spellingShingle | Robert Pokoo Shuchao Ren Qingyi Wang Christy M. Motes Timothy D. Hernandez Sayvan Ahmadi Maria J. Monteros Yun Zheng Ramanjulu Sunkar Genotype- and tissue-specific miRNA profiles and their targets in three alfalfa (Medicago sativa L) genotypes BMC Genomics |
| title | Genotype- and tissue-specific miRNA profiles and their targets in three alfalfa (Medicago sativa L) genotypes |
| title_full | Genotype- and tissue-specific miRNA profiles and their targets in three alfalfa (Medicago sativa L) genotypes |
| title_fullStr | Genotype- and tissue-specific miRNA profiles and their targets in three alfalfa (Medicago sativa L) genotypes |
| title_full_unstemmed | Genotype- and tissue-specific miRNA profiles and their targets in three alfalfa (Medicago sativa L) genotypes |
| title_short | Genotype- and tissue-specific miRNA profiles and their targets in three alfalfa (Medicago sativa L) genotypes |
| title_sort | genotype and tissue specific mirna profiles and their targets in three alfalfa medicago sativa l genotypes |
| url | http://link.springer.com/article/10.1186/s12864-018-5280-y |
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